Contacts of the helix formed by residues 129 - 148 (chain B) in PDB entry 3QZS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL 3.4 22.9 - - - +
66B LEU* 3.6 34.5 - - + +
67B THR 4.1 11.9 - - - +
68B PRO* 4.5 2.0 - - + -
69B LEU* 3.6 11.8 - - - +
127B TYR* 4.1 1.4 - - - +
128B GLU* 1.3 91.5 + - + +
130B LEU* 1.3 66.9 + - - +
131B THR* 3.9 21.1 - - - +
132B GLU* 3.1 39.4 + - + +
133B PHE 3.6 3.1 + - - -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL 5.7 0.2 + - - -
67B THR 5.0 2.4 + - - -
69B LEU* 3.9 18.4 - - + +
77B LEU* 3.8 28.5 - - + -
129B LYS* 1.3 74.7 - - - +
131B THR* 1.3 67.3 + - + +
133B PHE* 3.1 8.9 + - + +
134B VAL* 2.9 35.1 + - + +
169B LEU* 4.2 6.3 - - + -
172B PHE* 3.8 21.5 - - + -
173B LYS* 3.8 39.7 - - + -
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 4.7 26.9 + - + +
129B LYS* 3.9 23.4 - - - +
130B LEU* 1.3 78.9 - - + +
132B GLU* 1.3 59.8 + - - +
134B VAL* 3.5 9.0 + - - +
135B ALA* 3.0 27.7 + - - +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 4.3 6.9 - - + +
127B TYR* 3.6 21.8 - - + -
128B GLU* 2.8 42.1 + - - +
129B LYS* 3.1 34.3 + - + +
131B THR* 1.3 79.3 - - - +
133B PHE* 1.3 65.7 + - - +
135B ALA* 3.4 7.2 + - - +
136B ASP* 3.1 20.1 + - - +
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.8 51.6 - - + -
80B VAL* 4.7 7.9 - - + -
81B LEU* 4.5 10.1 - - + -
118B MET* 3.5 28.5 - - + +
122B VAL* 3.9 18.8 - - + -
127B TYR* 3.4 31.9 - + + -
129B LYS 3.6 3.4 + - - +
130B LEU* 3.1 17.6 + - + +
132B GLU* 1.3 81.2 - - - +
134B VAL* 1.3 68.7 + - + +
136B ASP 3.3 1.9 + - - -
137B MET* 3.0 28.9 + - + +
165B PHE* 3.9 24.2 - + - -
169B LEU* 5.6 1.8 - - + -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 2.9 29.9 + - + +
131B THR* 3.8 8.5 - - - +
133B PHE* 1.3 79.9 - - + +
135B ALA* 1.4 56.3 + - - +
137B MET* 3.3 1.7 + - - +
138B THR* 2.9 43.2 + - + +
165B PHE* 4.3 16.2 - - + -
169B LEU* 3.9 38.4 - - + -
173B LYS* 5.4 2.9 - - - +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR 3.0 18.2 + - - +
132B GLU* 3.6 8.3 - - - +
133B PHE 3.2 0.2 - - - -
134B VAL* 1.4 75.0 - - - +
136B ASP* 1.3 65.5 + - - +
138B THR* 3.1 18.5 + - - -
139B ALA* 3.1 13.9 + - - +
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Residues in contact with ASP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B MET* 3.5 26.6 - - + +
118B MET* 3.7 11.2 - - + -
121B ARG* 2.8 32.2 + - - -
126B TYR* 5.2 1.8 + - - -
127B TYR* 2.6 37.5 + - - +
132B GLU 3.1 7.9 + - - +
133B PHE 3.7 7.0 - - - +
135B ALA* 1.3 80.2 - - - +
137B MET* 1.3 63.6 + - - +
139B ALA* 3.2 12.6 + - - +
140B ILE* 3.4 7.3 + - - +
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Residues in contact with MET 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 5.6 0.2 - - + -
81B LEU* 4.1 9.2 - - + -
84B LEU* 3.3 33.0 - - + -
115B LEU* 3.8 18.6 - - + -
118B MET* 3.6 29.1 - - + +
133B PHE* 3.0 28.7 + - + +
134B VAL 3.3 3.3 + - - +
136B ASP* 1.3 76.7 - - - +
138B THR* 1.3 62.3 + - - +
140B ILE* 3.0 23.3 + - - +
141B PHE* 3.5 17.9 - - + -
165B PHE* 3.6 43.3 - - + -
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 2.9 32.7 + - + +
135B ALA* 3.1 16.6 + - - -
136B ASP 3.2 0.2 - - - -
137B MET* 1.3 76.3 - - - +
139B ALA* 1.3 56.6 + - - +
141B PHE* 3.4 11.8 + - + +
142B ASP* 3.0 42.7 + - - +
162B GLU* 5.7 4.7 - - + +
165B PHE* 4.6 11.4 - - + -
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLU* 4.9 4.9 - - + +
113B MET* 4.5 9.2 - - + -
135B ALA 3.1 13.3 + - - +
136B ASP* 3.5 12.8 - - - +
137B MET 3.1 0.4 - - - -
138B THR* 1.3 76.2 + - - +
140B ILE* 1.3 60.0 + - - +
142B ASP* 4.4 6.7 - - - +
143B ASN* 2.9 48.6 + - - +
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 3.8 35.4 - - + -
113B MET* 3.5 35.7 - - + +
114B ASP* 3.4 27.1 - - - -
115B LEU* 3.6 23.1 - - + -
118B MET* 3.7 18.2 - - - -
136B ASP 3.4 2.6 + - - +
137B MET* 3.0 12.8 + - - +
139B ALA* 1.3 78.6 - - - +
141B PHE* 1.3 72.0 + - + +
143B ASN* 4.2 2.9 - - - +
144B CYS* 3.3 21.8 + - - +
16D ALY 5.9 0.3 - - - +
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 4.2 2.9 - - + -
93B PHE* 4.7 4.3 - + - -
115B LEU* 6.1 0.2 - - + -
137B MET* 3.5 47.5 + - + -
138B THR* 3.4 10.4 + - + +
139B ALA 3.3 0.2 - - - -
140B ILE* 1.3 90.1 - - + +
142B ASP* 1.3 65.9 + - - +
144B CYS* 3.3 7.2 + - - +
145B ARG* 3.1 46.8 + - - +
158B ALA* 4.0 19.2 - - + +
161B LEU* 3.7 44.9 - - + -
162B GLU* 3.7 30.7 - - + +
165B PHE* 4.1 9.6 - + + -
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Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B THR* 3.0 34.3 + - - +
139B ALA* 4.2 4.6 - - - +
141B PHE* 1.3 73.4 - - - +
143B ASN* 1.3 62.4 + - - +
145B ARG* 2.9 29.0 + - - +
146B TYR* 2.9 29.7 + - - +
162B GLU* 4.4 1.6 - - - +
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Residues in contact with ASN 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR* 3.8 17.4 + - - +
109B ILE* 3.5 27.2 - - + +
111B GLU* 2.9 29.9 + - - +
112B PRO* 3.7 6.1 - - - +
113B MET 3.8 7.9 + - - +
139B ALA* 2.9 31.1 + - - +
140B ILE* 4.2 3.5 - - - +
142B ASP* 1.3 76.8 - - - +
144B CYS* 1.3 64.1 + - - +
146B TYR* 3.4 8.4 + - - +
147B TYR* 3.0 26.0 + - - +
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Residues in contact with CYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PHE* 3.6 24.0 - - + -
105B TYR* 5.0 0.8 + - - -
140B ILE 3.3 14.2 + - - +
141B PHE 3.5 9.0 - - - +
143B ASN* 1.3 80.8 - - - +
145B ARG* 1.3 57.2 + - - +
148B ASN* 3.0 53.0 + - - +
154B PHE* 3.3 33.9 - - - -
155B TYR* 4.2 1.0 - - - -
158B ALA* 3.8 8.3 - - + -
16D ALY 3.8 11.2 - - + +
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B PHE* 3.1 19.9 + - - +
142B ASP* 2.9 28.9 + - - +
144B CYS* 1.3 73.7 - - - +
146B TYR* 1.3 63.6 + - - +
148B ASN 3.4 4.9 - - - +
155B TYR* 3.6 38.1 - - + +
158B ALA* 3.8 26.8 + - + -
159B GLU* 3.0 31.1 + - - +
162B GLU* 2.6 42.9 + - - +
19D ARG* 2.8 28.8 + - - -
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Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 4.0 26.5 - - + -
109B ILE* 3.7 17.7 - - + -
142B ASP 2.9 18.1 + - - +
143B ASN* 3.5 10.3 - - - +
145B ARG* 1.3 76.6 - - - +
147B TYR* 1.3 57.1 + - - +
18D HIS* 3.6 11.9 - + - -
19D ARG* 3.2 18.7 - - - +
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Residues in contact with TYR 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA* 4.1 9.0 - - - +
104B ASP* 2.3 33.4 + - - -
105B TYR* 3.8 40.8 - + + -
108B VAL* 3.8 19.3 - - + -
109B ILE* 4.2 5.2 - - + -
143B ASN 3.0 17.0 + - - +
144B CYS* 4.9 0.2 - - - -
146B TYR* 1.3 78.8 - - - +
148B ASN* 1.3 80.4 + - - +
16D ALY 3.5 25.8 + - + -
17D ARG* 3.6 17.3 - - - -
18D HIS* 2.9 39.0 + - + -
19D ARG* 2.8 27.0 + - - +
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Residues in contact with ASN 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B CYS* 3.0 30.2 + - - +
145B ARG 3.4 9.2 - - - +
147B TYR* 1.3 90.9 - - - +
149B PRO* 1.3 71.4 - - + +
152B SER* 3.5 14.5 - - - +
154B PHE* 3.7 18.3 - - + +
155B TYR* 3.5 8.3 - - + +
16D ALY 2.9 51.7 + - - +
17D ARG 4.4 4.9 + - - +
19D ARG* 3.2 14.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il